Monday, 23 March 2015

Species traits in multivariate analysis

The March Eco-Stats Lab (Friday 27th, 2pm, Bioscience level 6) will be on incorporating species traits into multivariate analysis (or equivalently, community level models), using some functions recently added to the mvabund package.

Often ecologists collect data (especially abundance or presence-absence data) simultaneously across many taxa, with the intention of studying what occurs where (and why). This tutorial focusses on the why - methods to help us move towards a functional explanation of community abundances. McGill et al (2006) and Shipley (2010) argue passionately for the need for this.

A common strategy in any field looking at "why" is to look for predictor variables that can explain the response. In the case of studying why some taxa are abundant at a site while others are not, the relevant predictors are species traits. These come in a matrix, different traits in different columns, different taxa in different rows.

We will explore methods for using such a matrix of traits in a multivariate analysis, using the mvabund package (version 3.10.1 or later).  Full details here:
We will also discuss the relationship of these methods with standard analysis of multivariate abundance data, SDMs, and Bill Shipley's CATS models.

*** Note you need mvabund 3.10.1 or later... ***

UPDATE (13/5/15): mvabund 3.10.4 is now available from CRAN.  It has a formula argument for more control of the traitglm model you fit, and composition and col.intercepts arguments to control whether or not you include row/column effects in the model (to focus on relative abundance), and a block resampling option on anova.traitglm (useful for example if you have repeated measures).

Congratulations Francis!

In the last few weeks Francis Hui has pulled off two big results:
- his PhD has been awarded, with his thesis going through without changes, but with plenty of complements.
- he was awarded the 2015 E&ERC prize for best student paper for the below article in the Journal of the American Statistical Association:

Well done Francis!  Super effort.  He is currently working on a post-doc at ANU with Alan Welsh and Samuel Mueller, developing new methodology for mixed models.